RegulonDB RegulonDB 10.8: Gene Form
   

ybcN gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybcM ybcN ybcO ninE ylcH rusA terminator ybcNp5 ybcNp5 ybcNp6 ybcNp6 TSS_683 TSS_683

Gene      
Name: ybcN    Texpresso search in the literature
Synonym(s): ECK0538, G6303, b0547
Genome position(nucleotides): 572466 --> 572921 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.44
External database links:  
ASAP:
ABE-0001874
ECHOBASE:
EB3395
OU-MICROARRAY:
b0547
PortEco:
ybcN
STRING:
511145.b0547
COLOMBOS: ybcN


Product      
Name: DLP12 prophage; DNA base-flipping protein
Synonym(s): YbcN
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 17.433
Isoelectric point: 7.497
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
molecular_function GO:0003697 - single-stranded DNA binding
GO:0005515 - protein binding
GO:0000405 - bubble DNA binding
biological_process GO:0006298 - mismatch repair
External database links:  
ECOCYC:
G6303-MONOMER
ECOLIWIKI:
b0547
INTERPRO:
IPR036619
PRIDE:
Q47269
REFSEQ:
NP_415079
SMR:
Q47269
UNIPROT:
Q47269


Operon      
Name: ybcN-ninE-ybcO-rusA-ylcG         
Operon arrangement:
Transcription unit        Promoter
 


RNA cis-regulatory element    
Attenuation: Translational


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_683 571937 forward nd [RS-EPT-CBR] [1]
  promoter ybcNp6 572314 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter ybcNp5 572319 forward Similarity to the consensus
Read more >
[ICWHO] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78


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